We started with the gold standard canine genotyping platform—then we made it better
How did you design your SNP chip? We started with the gold standard canine genotyping platform, the CanineHD SNP chip, and added a number of proprietary probes that specifically queried mutations that affect certain traits and disease risks.
What percentage of the genome does the Embark chip represent?
The markers on our chip are evenly dispersed across the entire canine genome. We query over 200,000 unique genetic sequences. The dog's haploid genome is about 2,500,000,000 base pairs. (Other than the sperm and egg, all other cells in our body are diploid, carrying two copies of our genome.) So we cover about 8% of the genome.
Why can't you just sequence the whole genome? To maximize having every possible mutation in a dog's genome that could contribute to disease, we'd have to sequence the dog's entire genome. That's 6,000,000,000 bases to sequence, and at this time that would cost about $1,000 a dog just for laboratory processing—meaning commercially you're looking on average at about $2,000, if not more! This is an improvement, though: Whole genome sequencing has gone from tens of thousands of dollars to close to a thousand dollars in the past ten years. The SNP chip that Embark uses is far more cost-effective and is still highly informative.
Can we ever be sure we have found all the bad mutations in a species? Well, not really. Even between individuals of a breed, you can expect them to be a little different—around 0.01% different—in base pair sequence simply due to spontaneous mutations. Mutations can be bad, but they are also the source of the amazing variation that we see in dogs.
But how can we ever identify all the causative mutations? Honestly, I don't think there are many diseases that have just one causative mutation. Many previous genome-wide association studies for complex diseases, such as hip dysplasia, autoimmune disease, and idiopathic epilepsy, indicate that there are lots of genetic variants working together, not just one variant. These variants result in increased disease risk. In this model, a high density genotyping platform like Embark's allows us to to see linked patterns of mutations, called haplotypes, that are associated with increased disease risk.